Equine Colour Genetics
General Information
Genetic Shorthand
©CHETAR ARABIANS 2006 - 2010
Website Designed & Maintained By Kielee Hawtin
Introduction to Genetic Shorthand
The Written Sequence
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Only the genes affecting the outcome colour are represented in the written sequence

Genetic Shorthand Abbreviations
Genetics can be considered as having a language "all of its' own".
Rather than writing in full the name of the gene locus, followed by the name of the allele at the first chromosome locus, followed by the name of the second chromosome locus, along with the allelic forms and so on, a series of shorthand abbreviations are used that together form a simplified, shorter written code for an individuals' genotype. This page explains the way in which the genetic shorthand is written, and details the abbreviations used in the coded genotype.

As already discussed, the genotype for colour is a set sequence of genes occurring on chromosomes that every horse possesses. The genes and their sequence, the "string" of genes, are always the same in all individuals. It is the different alleles and the various allelic combinations that occur in pairs at each gene locus, to make up each of the gene pairings, that give us the multitude of horse colours we see.
This same sequence of genes is used when we write the genotype for colour in shorthand as a visual reference aid.
Each gene is appears in a certain order when we write the genotype in shorthand
Genetic shorthand consists of a series of abbreviations and symbols representitive of the gene loci and the alleles present in the gene pairing.
The gene locus abbreviation is written first, followed by the an abbreviation and/or symbol in superscript denoting the allele present at that gene loci.
Immediately following this gene locus abbreviation + allelic representation, the same gene locus abbreviation is written once more, followed by the superscript representation of the second allele occurring at that gene locus.
These four abbreviated gene and allele representations form the first gene [pairing] at the specified locus.
Each subsequent gene - the locus followed by the allele/s that form it x 2 - in the sequence is represented in the same format as above, with a comma followed by a single space separating each of the genes.
Each gene locus has a specific abbreviation, usually an initial or the first few letters of the gene locus name. As the gene locus is always the same in all individuals, the gene locus abbreviation in shorthand is the same in all individuals.

The alleles, however, have various representations dependant upon the alleles possessed by an individual at each specific gene locus. The abbreviations and symbols used to denote specific allelic forms can be, and often are, the same, which is why it is so important to include the gene locus abbreviation.
For example, wild type alleles, which occur at more than one gene locus, are always represented by a + symbol.
Also, in circumstances where an allele is unknown, or unimportant, symbols are used to represent these, in which case the gene locus abbreviation also becomes important.

For the above reasons and more, the gene locus is included in formal genetic shorthand.
It should be noted that there are often many cases where you will find that only the allelic combinations are represented. These cases are usually always limited to only one to a couple of gene respresentations at most though, and any extensive shorthand genotype will always have the gene locus representations included as they are paramount to being able to understand extensive written genotypes.
It can become quite convoluted trying to grasp genetic shorthand when switching back and forth, so I do recommend practicing the method of locus + allele.

While all horses possess all of the same genes, almost all horses possess allelic combinations at some genes that have no affect on the final outcome colour of the horse. It can be assumed that when a written genotype does not contain certain genes, that those certain genes have had no effect on the outcome colour, and that the horse possesses certain 'no affect' homozygous alleles at those certain gene locus.

With that being said, all horse colours begin with a Base Colour, controlled by the Extension Locus/Gene and the Agout Locus/Gene [See Base Colours page for more information on these two prerequisite genes for horse colour] and so all shorthand written genotypes will always include, and usually begin with, the denotations of the Extension Locus, and the alleles that occur there, and the Agouti Locus, and the alleles that occur there.
Gene Locus Abbreviations
Allelic Abbreviations
Genetic Shorthand Symbols
+ Denotes Wild Type Allele
The following table outlines the loci of individual genes and the shorthand abbreviations used when writing the genotype.
The following table further illustrates the abbreviations used to denote Dominant and Recessive Alleles present at each locus.
The following table further elaborates on those above to illustrate the additional symbols [I've] used in writing the genotypes for colour.
It should be noted that [some of] the symbols below aren't considered universal and are more of a personal preference.
The Punnet Square
The Punnet Square is essentially a simple tool used to determine the genetic inheritance possibilities at each gene loci.
Used with genetic shorthand abbreviations, the Punnet Square calculates the possible colours that progeny can inherit from the sire and dam when the genotype of both parents is known or is able to be determined by previous progeny and pedigree.
Below is an example of the first step in calculating the locus genotype possibilities at the Extension Gene - Writing in the sire and dams genotype.
The first horizontal row illistrates the sires genotype at the Extension Locus - [EeEe], which is the genotype for Chestnut.
The first vertical row illustrates the dams' genotype at the Extension Locus - [EEEe], which is not Chestnut [Bay or Black based].
Sires' Genotype
Dams' Genotype {
The four remaining cells in the table are used to combine the adjacent horizontal and vertical alleles of the sire and dam to give the possible combinations.
The second row, first column allele of [EE] from the dams' genotype is combined with the second column, first row allele of [Ee] from the sires' genotype to give the combination of [EEEe] as the progeny inheritance possibility. Each adjacent allele of the sire and dam is combined in the same way to give the end result as depicted in the table below.
In this case there is 2 in 4 chance - ie. 50% chance - that the progeny will be Chestnut based - [EeEe] and a 2 in 4 chance - ie. 50% chance - that the progeny will not be Chestnut based [ie. Bay or Black based] - [EEEe]
} Possible Progeny Inheritance

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Gene Name Gene Locus Gene/Locus Abbreviation
Extension Gene Extension Locus E
Agouti Gene Agouti Locus A
Grey Gene   G
Cream Gene Albino Locus Cr
     
Sabino Overo Gene [possibly] Kit Locus Sb
Champagne Gene   Ch
Silver [Dapple] Gene Silver Dapple Locus Z
Roan Kit Locus Rn
Rabicano unknown Rb
Tobiano Kit Locus T
Frame Overo Gene Frame Locus Fr
Appaloosa [Leopard] Complex unknown Lp
     
     
     

 

 

 

 

Gene Gene/Locus Abbreviation Locus + Dominant Allelic Abbreviation Locus + Recessive Allelic Abbrevation
Extension E E+ or EE & ED Ee
Agouti A AA & A+ Aa
Grey G GG G+
Sabino Overo Sb Sb1 & Sb+ Sbns
Frame Overo Fr FrF Fr+
Splashed White Overo Spl SplS Spl+
Tobiano T TT T+
Cream Cr CrCr Cr+
Rabicano Rb Rb+ Rbnr
[True] Roan Rn RnRn Rn+
Dun Dn Dn+ Dnnd
Champagne Ch ChC Ch+
Silver [Dapple] Z ZZ Z+
Appaloosa [Leopard] Complex Lp LpL Lp+
Flaxen unknown unknown unknown
Pangare Pa Pa+ Panp
Sooty unknown unknown unknown
Shade unknown unknown unknown

 

 

 

 

 

 

Symbol Symbol Name Represents
+ Addition Symbol Wild Type Allele
- Hyphen Unknown or Unimportant Allele
, Comma Separates Gene Pairs
x Multiplication Symbol Depicts Matings Between Horses
[ ] Brackets Genotypes Enclosed Within
> 'Greater Than' Symbol Inherited By Progeny
< 'Less Than' Symbol Inherited From Sire/Dam
// Forward Slash x 2 Separates Multiple Breedings

 

 

 

 

 

 

 

 

 

 

  Ee Ee
EE    
Ee    

 

 

 

 

  Ee Ee
EE EEEe EEEe
Ee EeEe EeEe